I love the 5 speeds but they are harder and harder to find.
My last 4 cars were 5 speeds and they last.
Americans seem to love expensive toys in their cars that break and cost a lot to fix.
Not only that: A few years ago my tranny went out in my Jeep. None of the repair shops would touch a manual transmission. I had to find a shade-tree backyard mechanic to rebuild it.
Also, our Driver's Ed cars were brand new '65 Chevys with 3 speed on the column.
My Shelby GT500 has a 6 speed and is a joy to drive.
My recent experience has been that they generally need to be ordered. The larger manufacturers all still offer manuals -- Honda, Toyota, BMW, Porsche, Audi, VW -- even Ford and GM do.
Manufacturers seem to be trending towards offering 6-speeds as the standard manual transmission, often making it a "no cost option" vs. an automatic. Buyers who want manual transmissions generally know what they want -- including colors, options, etc. and aren't likely to find exactly what they want on a dealer's lot. Easier for everyone to just order the car. Even my "Ultimate Driving Machine" BMW dealer had only one manual transmission demonstrator for me to try. But I had absolutely no trouble ordering one.
My "winter beater" is a Volvo with >200k miles, the original transmission, and still the original clutch. I've commuted in Washington DC and NYC with cars with stick shifts. True, the traffic was miserable -- but that would be the case with or without a manual transmission.
Manuals are more fun to drive, get better gas mileage, and are cheaper to buy and maintain... I'll give up my stick shift when they pry it out of my cold, dead hand!
Increased safety because of immunity from carjackers who never learned how to drive one is just icing on the cake.